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Bioinformatics Advance Access originally published online on May 27, 2004
Bioinformatics 2004 20(16):2886-2888; doi:10.1093/bioinformatics/bth325
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Bioinformatics vol. 20 issue 16 © Oxford University Press 2004; all rights reserved.

Applications Note

CoPS: Comprehensive Peptide Signature Database

Tulika Prakash , Mamta Khandelwal , Dipayan Dasgupta , Debasis Dash * and Samir K. Brahmachari

G.N.R. Knowledge Center for Genome Informatics, Institute of Genomics and Integrative Biology, (Formerly Centre for Biochemical Technology), CSIR, Delhi University Campus, Mall Road, Delhi 110 007, India

Received on October 22, 2003; revised on April 16, 2004; accepted on April 28, 2004
Advance Access Publication May 27, 2004

Summary: We present the development of a Comprehensive database of 12 076 invariant Peptide Signatures (CoPS) derived from 52 bacterial genomes with a minimum occurrence in at least seven organisms. These peptides were observed in functionally similar proteins and are distributed over nearly 1250 different functional proteins. The database provides function, structure and occurrence in biochemical pathways of the proteins containing these signature peptides. It houses additional information on the signature peptides, such as identical match in other motif/pattern (e.g. PROSITE, BLOCKS, PRINTS and Pfam) databases and the database of interacting proteins, human proteome and mutation effect on these signature peptides. There is a wide applicability of this database in the identification of critical functional residues in proteins. The database also facilitates the identification of folding nucleus/structural determinants in proteins and functional assignment to yet unknown proteins. We demonstrate functional assignment to 2605 hypothetical proteins in bacterial genomes and 112 unknown proteins in human using this database.

Availability: The database can be freely accessed through the following URL: http://203.195.151.46/copsv2/index.html or http://203.90.127.70/copsv2/index.html

Supplementary information: http://203.195.151.46/copsv2/aboutcops.html and http://203.90.127.70/copsv2/aboutcops.html

Contact: ddash{at}igib.res.in

* To whom correspondence should be addressed.


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